ebi-eva-common-pyutils 0.6.11__tar.gz → 0.6.13__tar.gz

{ebi_eva_common_pyutils-0.6.11 → ebi_eva_common_pyutils-0.6.13}/CHANGELOG.md

@@ -2,6 +2,17 @@
 Changelog for ebi_eva_common_pyutils
 ===========================
 
+## 0.6.13 (2025-03-05)
+----------------------
+
+- Update spring properties to use mongo connection string with retryWrites=true
+
+## 0.6.12 (2025-01-21)
+----------------------
+
+- Added new properties in clustering job to run clustering qc duplicate rs accession job
+
+
 ## 0.6.11 (2024-11-15)
 ----------------------
 

{ebi_eva_common_pyutils-0.6.11 → ebi_eva_common_pyutils-0.6.13}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: ebi_eva_common_pyutils
-Version: 0.6.11
+Version: 0.6.13
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache
@@ -20,3 +20,10 @@ Provides-Extra: eva-internal
 Requires-Dist: psycopg2-binary; extra == "eva-internal"
 Requires-Dist: pymongo; extra == "eva-internal"
 Requires-Dist: networkx<=2.5; extra == "eva-internal"
+Dynamic: classifier
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary

{ebi_eva_common_pyutils-0.6.11 → ebi_eva_common_pyutils-0.6.13}/ebi_eva_common_pyutils.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
-Name: ebi-eva-common-pyutils
-Version: 0.6.11
+Metadata-Version: 2.2
+Name: ebi_eva_common_pyutils
+Version: 0.6.13
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache
@@ -20,3 +20,10 @@ Provides-Extra: eva-internal
 Requires-Dist: psycopg2-binary; extra == "eva-internal"
 Requires-Dist: pymongo; extra == "eva-internal"
 Requires-Dist: networkx<=2.5; extra == "eva-internal"
+Dynamic: classifier
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary

{ebi_eva_common_pyutils-0.6.11 → ebi_eva_common_pyutils-0.6.13}/ebi_eva_common_pyutils.egg-info/SOURCES.txt

@@ -4,7 +4,7 @@ MANIFEST.in
 README.md
 setup.cfg
 setup.py
-/home/nkumar2/PycharmProjects/eva-common-pyutils/ebi_eva_internal_pyutils/archive_directory.py
+/tmp/ebi_eva_common_pyutils-v0.6.13-jtxab0mq/gitclone/ebi_eva_internal_pyutils/archive_directory.py
 ebi_eva_common_pyutils/__init__.py
 ebi_eva_common_pyutils/assembly_utils.py
 ebi_eva_common_pyutils/biosamples_communicators.py

{ebi_eva_common_pyutils-0.6.11 → ebi_eva_common_pyutils-0.6.13}/ebi_eva_internal_pyutils/spring_properties.py

@@ -55,14 +55,9 @@ class SpringPropertiesGenerator:
     def _mongo_properties(self):
         mongo_host, mongo_user, mongo_pass = get_mongo_creds_for_profile(
             self.maven_profile, self.private_settings_file)
+        username_with_password = f'{mongo_user}:{mongo_pass}@' if mongo_user is not None and mongo_pass is not None else ''
         return {
-            'spring.data.mongodb.host': mongo_host,
-            # Don't specify port if hosts already have the port encoded in them
-            # Also see https://github.com/EBIvariation/variation-commons/blob/329d4fa18da73bdad419ca5456b9897c059e33f0/variation-commons-mongodb/src/main/java/uk/ac/ebi/eva/commons/mongodb/utils/MongoClientURIBuilder.java#L44
-            'spring.data.mongodb.port': '' if ':' in mongo_host else 27017,
-            'spring.data.mongodb.username': '' if mongo_user is None else mongo_user,
-            'spring.data.mongodb.password': '' if mongo_pass is None else mongo_pass,
-            'spring.data.mongodb.authentication-database': 'admin',
+            'spring.data.mongodb.uri': f'mongodb://{username_with_password}{mongo_host}/?retryWrites=true&authSource=admin',
         }
 
     def _variant_load_job_tracker_properties(self):
@@ -141,7 +136,8 @@ class SpringPropertiesGenerator:
         """Properties for accessioning pipeline."""
         return self._format(
             self._common_accessioning_clustering_properties(assembly_accession=target_assembly,
-                                                            read_preference='secondaryPreferred', chunk_size=chunk_size),
+                                                            read_preference='secondaryPreferred',
+                                                            chunk_size=chunk_size),
             {
                 'spring.batch.job.names': 'CREATE_SUBSNP_ACCESSION_JOB',
                 'parameters.assemblyReportUrl': self._format_str('file:{0}', assembly_report),
@@ -157,8 +153,8 @@ class SpringPropertiesGenerator:
         )
 
     def get_clustering_properties(self, *, read_preference='primary', job_name=None, source_assembly='',
-                                  target_assembly='', rs_report_path='', projects='',
-                                  project_accession='', vcf=''):
+                                  target_assembly='', rs_report_path='', rs_acc_file='', duplicate_rs_acc_file='',
+                                  projects='', project_accession='', vcf=''):
         """Properties common to all clustering pipelines, though not all are always used."""
         return self._format(
             self._common_accessioning_clustering_properties(assembly_accession=target_assembly,
@@ -170,6 +166,8 @@ class SpringPropertiesGenerator:
                 'parameters.projectAccession': project_accession,
                 'parameters.vcf': vcf,
                 'parameters.rsReportPath': rs_report_path,
+                'parameters.rsAccFile': rs_acc_file,
+                'parameters.duplicateRSAccFile': duplicate_rs_acc_file,
             }
         )
 
@@ -263,7 +261,8 @@ class SpringPropertiesGenerator:
             'logging.level.org.springframework': 'INFO',
         }
 
-        merge = {**self._common_properties(read_preference=read_preference, chunk_size=100), **props, **job_tracker_properties}
+        merge = {**self._common_properties(read_preference=read_preference, chunk_size=100), **props,
+                 **job_tracker_properties}
         return merge
 
     def get_accession_import_properties(self, opencga_path, read_preference='secondaryPreferred'):

{ebi_eva_common_pyutils-0.6.11 → ebi_eva_common_pyutils-0.6.13}/setup.py

@@ -7,7 +7,7 @@ setup(
     name='ebi_eva_common_pyutils',
     scripts=[os.path.join(os.path.dirname(__file__), 'ebi_eva_internal_pyutils', 'archive_directory.py')],
     packages=find_packages(),
-    version='0.6.11',
+    version='0.6.13',
     license='Apache',
     description='EBI EVA - Common Python Utilities',
     url='https://github.com/EBIVariation/eva-common-pyutils',